Tutorials

These tutorial pages suppose you are comfortable with the basic concepts of MEG/EEG analysis and source imaging. If you're not, we encourage you to read some background literature.

Get started

The easiest way to get started with Brainstorm is to read and follow carefully these introduction tutorials. In just a few hours, you will be introduced to the essential features of the application.

Starting a new study

1. Create a new protocol

2. Import the subject anatomy

3. Explore the anatomy

Reviewing and pre-processing

1. Channel file and coregistration MEG-MRI

2. Continuous recordings [Under construction]

3. Montage editor [Under construction]

4. ?Multiple windows [Under construction]

5. Event markers [Under construction]

6. Stimulation delays [Under construction]

7. Frequency filters [Under construction]

8. Bad channels [Under construction]

9. Artifact detection [Under construction]

10. Artifact cleaning with SSP [Under construction]

11. Additional bad segments [Under construction]

Epoching and averaging [Under construction]

1. Import epochs

2. Average response

3. Exploring the average response

4. 2D/3D topography

5. Colormaps

Source modeling [Under construction]

1. Head model

2. Noise covariance

3. Source estimation

4. Scouts

Advanced topics [Under construction]

1. Time-frequency

2. Statistics

3. Connectivity

4. Phase-amplitude coupling

5. Advanced scripting

6. Complete tutorial script
7. Summary

Complete analysis of other datasets

1. EEG and epilepsy

2. MEG auditory tutorial

3. MEG median nerve (CTF) [Under construction]

4. MEG median nerve (Yokogawa/KIT)

5. MEG median nerve (Elekta-Neuromag) [Under construction]

6. MEG resting state

Advanced tutorials

Anatomy and registration

1. Brainstorm coordinate systems

2. MRI segmentation: FreeSurfer, BrainVISA, BrainSuite, CIVET

3. Using the anatomy templates [Under construction]

4. Warping default anatomy

5. Group studies: Subjects coregistration

6. Group studies: Averaging

7. Digitize EEG electrodes and head shape

8. Real-time head positioning in the CTF MEG system

Graphical scripting

1. Selecting files in the database

2. Full analysis with one script

3. How to write your own process

Source modeling

1. BEM with OpenMEEG

2. Volume source estimation

3. Computing and displaying dipoles

4. Beamforming methods [Under construction]

5. Maximum Entropy on the Mean (MEM) [Under construction]

Functional connectivity

1. Phase-amplitude coupling

Statistics

1. Export volume source maps to SPM8 / SPM12

2. Export surface source maps to SPM12

Other useful how-to's

1. How to cite Brainstorm in your publications

2. Known bugs

3. ?MEG analysis guidelines for McGill

Examples

1. This video illustrates how Brainstorm can be used for studying amygdala activity:
   How to Detect Amygdala Activity with Magnetoencephalography using Source Imaging
   Authors: Balderston NL, Schultz DH, Baillet S, Helmstetter FJ

Background readings

These tutorial pages suppose you are comfortable with the basic concepts of MEG and EEG source imaging. If you're not, we engage you to read some background information, which will quickly help you getting up to speed with this field:

• A non-technical overview of MEG and EEG, with an emphasis on source modeling:
  Canada MEG Consortium

• Slides from a selection of educational courses:
  megcommunity.org

• Reference books:

  • MEG: An Introduction to Methods
    Editors: P Hansen, M Kringelbach, R Salmelin, Oxford University Press, 2010, 448 pages

  • The Oxford Handbook of Social Neuroscience
    Editors: J Decety, JT Cacioppo, Oxford University Press, 2011, 1128 pages
    A draft version of the MEG chapter by Sylvain Baillet can be found here.

• Good practice for conducting and reporting MEG research, Gross et al, Neuroimage, 2013

• You can also ask us to come and organize a training session at your institution, or visit us to obtain training (McGill's Montreal Neurological Institute).

Now you are well equipped to go through the software tutorial, Enjoy!